Align 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase; 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase; HHED aldolase; 4-hydroxy-2-ketoheptane-1,7-dioate aldolase; HKHD aldolase; EC 4.1.2.52 (characterized)
to candidate HSERO_RS01600 HSERO_RS01600 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Query= SwissProt::Q47098 (262 letters) >FitnessBrowser__HerbieS:HSERO_RS01600 Length = 250 Score = 125 bits (314), Expect = 9e-34 Identities = 76/235 (32%), Positives = 119/235 (50%), Gaps = 4/235 (1%) Query: 2 ENSFKAALKAGRPQIGLWLGLSSSYSAELLAGAGFDWLLIDGEHAPNNVQTVLTQLQAIA 61 EN + + + W+ + ++ AE++A +G+D + +D +H P ++ L LQAI+ Sbjct: 3 ENRLRTLFAQQQLALSGWVSMGNALLAEVIAHSGYDAVTVDLQHGPFSIDAALPMLQAIS 62 Query: 62 PYPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRATRYPPAGIRGVGSA 121 P+ P+VR S N +I +LLD G ++ P++ A +A VRA Y P G R G Sbjct: 63 STPAVPLVRCSENSLGEINKLLDAGAYGVICPLINTAADAERFVRACHYSPRGGRSYGP- 121 Query: 122 LARASRWNRIPDYLQKANDQMCVLVQIETREAMKNLPQILDVEGVDGVFIGPADLSADMG 181 AR + DY AN + L IETRE N IL +DG+FIGP+DL+ ++G Sbjct: 122 -ARGFLYGG-ADYFTHANATLLTLAMIETREGYANAEAILQTPDLDGIFIGPSDLAIELG 179 Query: 182 YAGNP-QHPEVQAAIEQAIVQIRESGKAPGILIANEQLAKRYLELGALFVAVGVD 235 A + + AI+ + R+ GK GI ++A+R +G V G D Sbjct: 180 LAPDAYDDVRLNEAIDHLLALARKLGKYVGIFAGTMEMAQRMKGIGMDLVVPGTD 234 Lambda K H 0.317 0.133 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 148 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 262 Length of database: 250 Length adjustment: 24 Effective length of query: 238 Effective length of database: 226 Effective search space: 53788 Effective search space used: 53788 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory